Diversity of aromatic hydroxylating dioxygenase genes in mangrove microbiome and their biogeographic patterns across global sites

Abstract

Aromatic hydrocarbons (AH), such as polycyclic aromatic hydrocarbons, are compounds largely found in nature. Aromatic‐ring‐hydroxylating dioxygenases (ARHD) are proteins involved in AH degradation pathways. We used ARHD functional genes from an oil‐impacted mangrove area and compared their diversity with other sites around the world to understand the ARHD biogeographic distribution patterns. For this, a comprehensive database was established with 166 operational protein families (OPFs) from 1,758 gene sequences obtained from 15 different sites worldwide, of which twelve are already published studies and three are unpublished. Based on a deduced ARHD peptide sequences consensus phylogeny, we examined trends and divergences in the sequence phylogenetic clustering from the different sites. The taxonomic affiliation of the OPF revealed that Pseudomonas, Streptomyces, Variovorax, Bordetella and Rhodococcus were the five most abundant genera, considering all sites. The functional diversity analysis showed the enzymatic prevalence of benzene 1,2‐dioxygenase, 3‐phenylpropionate dioxygenase and naphthalene 1,2‐dioxygenase, in addition to 10.98% of undefined category ARHDs. The ARHD gene correlation analysis among different sites was essentially important to gain insights on spatial distribution patterns, genetic congruence and ecological coherence of the bacterial groups found. This work revealed the genetic potential from the mangrove sediment for AH biodegradation and a considerable evolutionary proximity among the dioxygenase OPFs found in Antarctica and South America sites, in addition to high level of endemism in each continental region.

Exploring bacterial functionality in mangrove sediments and its capability to overcome anthropogenic activity

“…These metabolic pathways were presented at these sites (Cabral et al, 2018). Recently, genes encoding aromatic hydroxylating dioxygenase genes were detected in the same oil-impacted areas used at this study (BrMgv02) using a clone library and metagenomic/metatranscriptomic methodology (Sousa et al, 2017;Cabral et al, 2018).…”

Laboratory-Scale Biodegradation of Fuel Oil No. 6 in Contaminated Soils by Autochthonous Bacteria

“…It has been reported that microorganisms from the Pseudomonas group had a big pathway of degradation for many types of pollutants [34]. This microbial group can degrade a wide variety of hydrophilic and hydrophobic compounds, including polycyclic aromatic hydrocarbons (PAHs) [35][36][37]. On the other hand, Bacillus, Rhodococcus, and Actinomyces strains can also degrade PHAs [37][38][39].…”

“…This microbial group can degrade a wide variety of hydrophilic and hydrophobic compounds, including polycyclic aromatic hydrocarbons (PAHs) [35][36][37]. On the other hand, Bacillus, Rhodococcus, and Actinomyces strains can also degrade PHAs [37][38][39]. The isolated strains from the soils of the three types of experiments were cultivated in M9 minimum agar added with FO6, in order to observe if they can use TPH present in FO6 as carbon source (Figure 5).…”

Characterization and Hydrocarbon Degradation Potential of Variovorax sp. Strain N23 Isolated from the Antarctic Soil

“…The strains of the genus Variovorax are widely distributed in nature, from temperate to Polar regions, and some members are psychrophilic [7,8]. They were isolated from a variety of ecological habitats, including Antarctic lichen, plant rhizosphere, sewage, and contaminated soil with chemicals [9][10][11][12].…”

“…It exhibits diverse metabolic features. More importantly, it is known for its metabolism of organic pollutants, including PAHs and chlorophenol [7,11]. Recently, Ghimire et al reported that Variovorax sp.…”